Exam 5 Bio 305

Promoter

contains TATA box and where RNA Pol II and general transcription factors bind to start transcription

Promoter-proximal elements

DNA sequences near the promoter that bind regulatory proteins

Enhancers

DNA elements that bind activators and increase transcription

Silencers

DNA elements that bind repressors to decrease transcription

Locus Control Regions (LCRs)

control expression of multiple related genes such as the β-globin cluster

Insulators

DNA sequences that block enhancers from affecting the wrong genes and help form DNA loops

General Transcription Factors (GTFs)

proteins required for all RNA Pol II gene transcription

Activators

proteins that bind enhancers to increase transcription

Repressors

proteins that bind silencers to decrease transcription

Pioneer factors

transcription factors that can bind tightly packed DNA to initiate transcription changes

Enhanceosomes

protein complexes at enhancers that bend DNA to help recruit transcription machinery

GAL4

yeast activator that binds UASG to activate GAL genes

GAL80

repressor that binds GAL4 and prevents activation when galactose is absent

GAL3

protein that binds galactose and inactivates GAL80 allowing GAL4 to activate transcription

Mig1 + Tup1

proteins that repress GAL genes in the presence of glucose

Euchromatin

loosely packed chromatin that allows active transcription

Heterochromatin

tightly packed chromatin that silences genes

Constitutive heterochromatin

always compact and silenced

Facultative heterochromatin

can switch between compact and open states

Nucleosomes

basic unit of chromatin with DNA wrapped around histone proteins

SWI/SNF

chromatin remodeling complex that opens chromatin by ejecting nucleosomes

ISWI

chromatin remodeling complex that repositions nucleosomes often repressing transcription

SWR1

inserts H2A.Z histone variant to loosen chromatin and promote transcription

Histone acetylation

modification by HATs that opens chromatin and activates transcription

Histone deacetylation

modification by HDACs that closes chromatin and represses transcription

H3K9me3

histone methylation mark associated with heterochromatin and gene silencing

H3K4me or H3K9Ac

histone modifications associated with euchromatin and active transcription

DNase I hypersensitive sites

regions of open chromatin that indicate active genes

ChIP

assay that detects protein binding to DNA in living cells

PHO5 high phosphate

gene off due to blocked promoter

PHO5 low phosphate

Pho4 activates transcription by recruiting acetylation and SWI/SNF removes nucleosomes

Barrier insulators

prevent spread of heterochromatin into euchromatic regions

TrxG proteins

maintain active gene expression

PcG proteins

maintain gene repression

Eukaryotic genome size

larger and more complex than prokaryotic genomes

Chromatin

DNA packaged with histones and proteins to fit into the nucleus

10-nm fiber

nucleosome fiber where DNA wraps around histone octamers

30-nm fiber

coiled structure of 10-nm fibers

Higher-order chromatin structure

further folding and anchoring of DNA to scaffolds

Eukaryotic gene regulation

more complex due to chromatin structure

Default gene expression in prokaryotes

permissive—RNA polymerase can access DNA unless blocked

Default gene expression in eukaryotes

restrictive—DNA is inaccessible unless chromatin is opened by regulatory protein

Epigenetic Inheritance

Inheritance of chromatin states (active or silent) from one cell generation to the next

Epigenetics

Study of inherited changes in gene expression not caused by changes in DNA sequence

Epigenetic Marks

Chemical modifications like DNA methylation and chromatin structure that regulate gene expression

Maintenance of Chromatin States

The process by which cells pass on chromatin memory during mitosis

Hemimethylated DNA

DNA after replication where only one strand is methylated

Maintenance Methylation

DNA methyltransferase adds methyl groups to the new strand after replication

Genomic Imprinting

Only one allele (mom's or dad's) is expressed; the other is silenced by DNA methylation

Dosage Compensation

Balances X-linked gene expression between males and females using chromatin changes

Position Effect Variegation (PEV)

Gene silencing caused by moving a gene near heterochromatin

Variegated Phenotype

A mosaic pattern of gene expression due to PEV

Su(var) Mutants

Suppress heterochromatin spread and increase gene activity

E(var) Mutants

Enhance heterochromatin spread and increase gene silencing

PEV Heritability

Silencing from PEV is mitotically inherited

PEV Example

Drosophila white+ gene moved near centromeric heterochromatin shows red and white patches in eyes

Facultative Heterochromatin

Chromatin that can switch between euchromatin and heterochromatin

PcG (Polycomb group)

Maintains gene repression through H3K27me3 and HDACs

TrxG (Trithorax group)

Maintains gene activation through H3K4 methylation and acetylation

Facultative Heterochromatin Example

PcG and TrxG regulate Drosophila Hox genes

Epigenetic Heritability

Inheritance of gene expression without DNA sequence changes

DNA Methylation (Heritability)

Maintained after replication by DNA methyltransferase

Histone Modification (Heritability)

Old histones help modify new histones during replication

Epigenetic Resetting

Most epigenetic marks are erased in germ cells

Genomic Imprinting Mechanism

Different methylation patterns on maternal vs. paternal chromosomes at ICRs

ICR (Imprinting Control Region)

Region that controls imprinting and has different methylation states

Insulator Function in Imprinting

Can block enhancers if ICR is unmethylated

IGF2 & H19 Example (Paternal)

ICR is methylated → IGF2 on

IGF2 & H19 Example (Maternal)

ICR is unmethylated → H19 on

Imprint Resetting

Imprints are erased and re-established in a sex-specific way

Significance of Imprinting

Gene expression and phenotype depend on parent of origin